TABLE 1.

Proteins that associate with lysosomes and directly modulate TLs in immune cells (iTLs), lysosome reformation (LR), and/or autophagy (aTLs).

	Protein name	Function	iTLs	LR	aTLs	Species	References
Cytoskeleton proteins	Kinesin-1	plus-end motor protein	✓	✓	?	mammals	(Hollenbeck and Swanson 1990; Du et al., 2016)
	Dynein	minus-end motor protein	✓	?	?	mammals	(Jordens et al., 2001; Mrakovic et al., 2012)
	Rab7	GTPase	✓	↓	✓	mammals, Drosophila	(Yu et al., 2010; Mrakovic et al., 2012); unpublished observation in Drosophila
	Arl8B	GTPase	✓	✓	?	mammals	Mrakovic et al. (2012)
	RILP	Rab7 effector	✓	?	?	mammals	Jordens et al. (2001)
	FYOC1	Rab7 effector	✓	?	?	mammals	Pankiv et al. (2010)
	ORP1L	Rab7 effector	✓	✓	?	mammals	Levin-Konigsberg et al. (2019)
	SKIP	Arl8B effector	✓	?	?	mammals	Mrakovic et al. (2012)
	ALG-2	EF-hand protein	✓	✓	?	mammals	Li et al. (2016)
	WHAMM	actin nucleation promoting factor	?	✓	?	mammals	Dai et al. (2019)
Lysosomal membrane proteins	LAMP-1	lysosome-associated membrane protein	✓	✓	?	mammals	(Vyas et al., 2007; Yu et al., 2010)
	SLC15A3	H+/oligopeptide symporter	✓	?	?	mammals	Nakamura et al. (2014)
	SLC15A4	H+/oligopeptide symporter	✓	?	?	mammals	Nakamura et al. (2014)
	Spinster	sugar transporter	?	✓	✓	mammals, Drosophila,C. elegans	(Rong et al., 2011; Murakawa et al., 2020; Dolese et al., 2021)
	TRPML	lysosomal Ca2+ channel	✓	✓	✓	mammals, Drosophila, C. elegans	(Li et al., 2016; Murakawa et al., 2020; Sun et al., 2020)
	V-ATPase	lysosomal H+ pump	?	?	✓	Drosophila,C. elegans	(Miao et al., 2020; Murakawa et al., 2020)
Lipid/sugar modifiers	PI3K	lipid kinase	?	↓	?	mammals	Munson et al. (2015)
	INPP5K	inositol phosphatase	?	✓	?	mammals	McGrath et al. (2021)
	PIP5K-1A and PIP5K-1B	lipid kinases	?	✓	?	mammals	Rong et al. (2012)
	PIP3Kβ	lipid kinase	?	✓	?	mammals	Sridhar et al. (2013)
Lysosomal membrane binding proteins	Clathrin	membrane binding	?	✓	✓	mammals,Drosophila	(Rong et al., 2012; Johnson et al., 2015)
	Syntaxin 17	SNARE	?	?	✓	Drosophila	Murakawa et al. (2020)
	BLOC1S1	biogenesis of lysosomal organelle complex-1	?	✓	?	mammals	Wu et al. (2021)
	SPG15	Spastizin	?	✓	?	mammals	Chang et al. (2014)
	SPG11	Spatacsin	?	✓	?	mammals	Chang et al. (2014)
	VCP	AAA+ ATPase	?	?	✓	Drosophila	Johnson et al. (2015)
	SVIP	VCP adapter	?	?	✓	Drosophila	Johnson et al. (2021)

(✓) indicates that the protein is required for lysosome tubulation in a particular context, (↓) indicates that downregulation of the protein is required for lysosome tubulation in a particular context, and (?) indicates that potential involvement of the protein has not been described or is unknown in a particular context.